public class XtandemParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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XtandemParameters()
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same
parameters.
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Advocate |
getAlgorithm()
Returns the identification algorithm.
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double |
getDynamicRange()
Returns the dynamic range for spectrum filtering.
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double |
getMaxEValue()
Returns the maximal e-value searched for.
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double |
getMaximumExpectationValueRefinement()
Returns the maximum expectation value to use for refinement.
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double |
getMinFragmentMz()
Returns the minimal fragment m/z.
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int |
getMinPeaksPerSpectrum()
Returns the minimal number of peaks per spectrum.
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double |
getMinPrecursorMass()
Returns the minimal precursor mass.
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int |
getnPeaks()
Returns the number of most intense peaks to consider.
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String |
getOutputResults()
Returns the output results filter.
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boolean |
getParentMonoisotopicMassIsotopeError()
Returns true if the parent ion mass tolerance is expanded by opening up
multiple tolerance windows centered on the first and second 13C isotope
peaks for a peptide.
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double |
getProteinPtmComplexity()
Returns the proteinPtmComplexity.
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String |
getSkylinePath()
Returns the skyline path.
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boolean |
isOutputHistograms()
Indicates whether histograms should be written in the result file.
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boolean |
isOutputProteins()
Indicates whether the protein bloc should be included in the export.
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boolean |
isOutputSequences()
Returns whether the protein sequences should be included in the protein
block of the export.
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boolean |
isOutputSpectra()
Indicate whether the spectra should be exported in the result file.
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boolean |
isPotentialModificationsForFullRefinment()
Indicates whether the refinement modifications should be used for the
full refinement.
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boolean |
isProteinQuickAcetyl()
Indicates whether the protein quick acetylation option should be
triggered.
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boolean |
isQuickPyrolidone()
Returns whether the quick pyrolidone option should be triggered.
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boolean |
isRefine()
Returns whether the second pass search should be triggered.
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boolean |
isRefinePointMutations()
Indicates whether point mutations should be looked for during the
refinement process.
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boolean |
isRefineSemi()
Indicates whether the semi enzymatic option of the second pass search
should be triggered.
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boolean |
isRefineSnaps()
Sets whether snAPs should be used during the refinement process.
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boolean |
isRefineSpectrumSynthesis()
Indicates whether the spectrum synthesis option should be used during the
refinement process.
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boolean |
isRefineUnanticipatedCleavages()
Returns whether the unanticipated cleavages option should be used during
the refinement process.
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boolean |
isStpBias()
Returns whether the stP bias should be triggered.
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boolean |
isUseNoiseSuppression()
Indicates whether noise suppression should be used when importing
spectra.
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void |
setDynamicRange(double dynamicRange)
Sets the dynamic range for spectrum filtering.
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void |
setMaxEValue(double maxEValue)
Sets the maximal e-value searched for.
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void |
setMaximumExpectationValueRefinement(double maximumExpectationValue)
Sets the maximum expectation value to use for refinement.
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void |
setMinFragmentMz(double minFragmentMz)
Sets the minimal fragment m/z.
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void |
setMinPeaksPerSpectrum(int minPeaksPerSpectrum)
Sets the minimal number of peaks per spectrum.
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void |
setMinPrecursorMass(double minPrecursorMass)
Sets the minimal precursor mass.
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void |
setnPeaks(int nPeaks)
Sets the number of most intense peaks to consider.
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void |
setOutputHistograms(boolean outputHistograms)
Sets whether histograms should be written in the result file
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void |
setOutputProteins(boolean outputProteins)
Sets whether the protein bloc should be included in the export.
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void |
setOutputResults(String outputResults)
Set the output results filter.
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void |
setOutputSequences(boolean outputSequences)
Sets whether the protein sequences should be included in the protein
block of the export.
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void |
setOutputSpectra(boolean outputSpectra)
Sets whether the spectra should be exported in the result file.
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void |
setParentMonoisotopicMassIsotopeError(boolean parentMonoisotopicMassIsotopeError)
Sets whether the parent ion mass tolerance is expanded by opening up
multiple tolerance windows centered on the first and second 13C isotope
peaks for a peptide.
|
void |
setPotentialModificationsForFullRefinment(boolean potentialModificationsForFullRefinment)
Sets whether the refinement modifications should be used for the full
refinement
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void |
setProteinPtmComplexity(double proteinPtmComplexity)
Set the proteinPtmComplexity.
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void |
setProteinQuickAcetyl(boolean proteinQuickAcetyl)
Sets whether the protein quick acetylation option should be triggered.
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void |
setQuickPyrolidone(boolean quickPyrolidone)
Sets whether the quick pyrolidone option should be triggered.
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void |
setRefine(boolean refine)
Sets whether the second pass search should be triggered.
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void |
setRefinePointMutations(boolean refinePointMutations)
Sets whether point mutations should be looked for during the refinement
process.
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void |
setRefineSemi(boolean refineSemi)
Sets whether the semi enzymatic option of the second pass search should
be triggered.
|
void |
setRefineSnaps(boolean refineSnaps)
Sets whether snAPs should be used during the refinement process.
|
void |
setRefineSpectrumSynthesis(boolean refineSpectrumSynthesis)
Sets whether the spectrum synthesis option should be used during the
refinement process.
|
void |
setRefineUnanticipatedCleavages(boolean refineUnanticipatedCleavages)
Sets whether the unanticipated cleavages option should be used during the
refinement process.
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void |
setSkylinePath(String skylinePath)
Sets the skyline path.
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void |
setStpBias(boolean stpBias)
Sets whether the stP bias should be triggered
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void |
setUseNoiseSuppression(boolean useNoiseSuppression)
Sets whether noise suppression should be used when importing spectra.
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String |
toString(boolean html)
Returns the parameters as a string.
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public double getDynamicRange()
public void setDynamicRange(double dynamicRange)
dynamicRange
- the dynamic range for spectrum filteringpublic int getnPeaks()
public void setnPeaks(int nPeaks)
nPeaks
- the number of most intense peaks to considerpublic double getMinPrecursorMass()
public void setMinPrecursorMass(double minPrecursorMass)
minPrecursorMass
- the minimal precursor masspublic double getMinFragmentMz()
public void setMinFragmentMz(double minFragmentMz)
minFragmentMz
- the minimal fragment m/zpublic int getMinPeaksPerSpectrum()
public void setMinPeaksPerSpectrum(int minPeaksPerSpectrum)
minPeaksPerSpectrum
- the minimal number of peaks per spectrumpublic boolean isProteinQuickAcetyl()
public void setProteinQuickAcetyl(boolean proteinQuickAcetyl)
proteinQuickAcetyl
- true if the protein quick acetylation option
should be triggeredpublic boolean isQuickPyrolidone()
public void setQuickPyrolidone(boolean quickPyrolidone)
quickPyrolidone
- the quick pyrolidone option should be triggeredpublic boolean isRefine()
public void setRefine(boolean refine)
refine
- true if the second pass search should be triggeredpublic boolean isStpBias()
public void setStpBias(boolean stpBias)
stpBias
- true if the stP bias should be triggeredpublic double getMaxEValue()
public void setMaxEValue(double maxEValue)
maxEValue
- the maximal e-value searched forpublic boolean isRefineSemi()
public void setRefineSemi(boolean refineSemi)
refineSemi
- true if the semi enzymatic option of the second pass
search should be triggeredpublic boolean isRefinePointMutations()
public void setRefinePointMutations(boolean refinePointMutations)
refinePointMutations
- true if point mutations should be looked for
during the refinement processpublic boolean isRefineSpectrumSynthesis()
public void setRefineSpectrumSynthesis(boolean refineSpectrumSynthesis)
refineSpectrumSynthesis
- true if the spectrum synthesis option
should be used during the refinement processpublic boolean isRefineUnanticipatedCleavages()
public void setRefineUnanticipatedCleavages(boolean refineUnanticipatedCleavages)
refineUnanticipatedCleavages
- true if the unanticipated cleavages
option should be used during the refinement processpublic double getMaximumExpectationValueRefinement()
public void setMaximumExpectationValueRefinement(double maximumExpectationValue)
maximumExpectationValue
- the maximum expectation value to use for
refinementpublic boolean isPotentialModificationsForFullRefinment()
public void setPotentialModificationsForFullRefinment(boolean potentialModificationsForFullRefinment)
potentialModificationsForFullRefinment
- true if the refinement
modifications should be used for the full refinementpublic String getSkylinePath()
public void setSkylinePath(String skylinePath)
skylinePath
- the skyline pathpublic boolean isOutputProteins()
public void setOutputProteins(boolean outputProteins)
outputProteins
- the protein bloc should be included in the exportpublic boolean isOutputSequences()
public void setOutputSequences(boolean outputSequences)
outputSequences
- true if the protein sequences should be included
in the protein block of the exportpublic boolean isOutputSpectra()
public void setOutputSpectra(boolean outputSpectra)
outputSpectra
- true if the spectra should be exported in the result
filepublic boolean isOutputHistograms()
public void setOutputHistograms(boolean outputHistograms)
outputHistograms
- true if histograms should be written in the
result filepublic boolean isUseNoiseSuppression()
public void setUseNoiseSuppression(boolean useNoiseSuppression)
useNoiseSuppression
- true if noise suppression should be used when
importing spectrapublic boolean isRefineSnaps()
public void setRefineSnaps(boolean refineSnaps)
refineSnaps
- true if snAPs should be used during the refinement
processpublic String getOutputResults()
public void setOutputResults(String outputResults)
outputResults
- the outputResults to setpublic double getProteinPtmComplexity()
public void setProteinPtmComplexity(double proteinPtmComplexity)
proteinPtmComplexity
- the proteinPtmComplexity to setpublic Advocate getAlgorithm()
IdentificationAlgorithmParameter
getAlgorithm
in interface IdentificationAlgorithmParameter
public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
IdentificationAlgorithmParameter
equals
in interface IdentificationAlgorithmParameter
identificationAlgorithmParameter
- the other
identificationAlgorithmParameterpublic String toString(boolean html)
IdentificationAlgorithmParameter
toString
in interface IdentificationAlgorithmParameter
html
- use HTML formattingpublic boolean getParentMonoisotopicMassIsotopeError()
public void setParentMonoisotopicMassIsotopeError(boolean parentMonoisotopicMassIsotopeError)
parentMonoisotopicMassIsotopeError
- the parentMonoisotopicMassIsotopeError to setCopyright © 2018. All rights reserved.